Magnesium in PDB 4fmm: Dimeric SEC14 Family Homolog 3 From Saccharomyces Cerevisiae Presents Some Novel Features of Structure That Lead to A Surprising "Dimer- Monomer" State Change Induced By Substrate Binding

The structure of Dimeric SEC14 Family Homolog 3 From Saccharomyces Cerevisiae Presents Some Novel Features of Structure That Lead to A Surprising "Dimer- Monomer" State Change Induced By Substrate Binding, PDB code: 4fmm was solved by Y.Yuan, W.Zhao, X.Wang, Y.Gao, L.Niu, M.Teng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.41 / 2.34
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	76.177, 76.914, 294.956, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.4

The binding sites of Magnesium atom in the Dimeric SEC14 Family Homolog 3 From Saccharomyces Cerevisiae Presents Some Novel Features of Structure That Lead to A Surprising "Dimer- Monomer" State Change Induced By Substrate Binding (pdb code 4fmm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Dimeric SEC14 Family Homolog 3 From Saccharomyces Cerevisiae Presents Some Novel Features of Structure That Lead to A Surprising "Dimer- Monomer" State Change Induced By Substrate Binding, PDB code: 4fmm:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Dimeric SEC14 Family Homolog 3 From Saccharomyces Cerevisiae Presents Some Novel Features of Structure That Lead to A Surprising "Dimer- Monomer" State Change Induced By Substrate Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dimeric SEC14 Family Homolog 3 From Saccharomyces Cerevisiae Presents Some Novel Features of Structure That Lead to A Surprising "Dimer- Monomer" State Change Induced By Substrate Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:24.2 occ:1.00 OD2 A:ASP73 2.6 22.2 1.0 O A:HOH537 2.7 16.5 1.0 O A:HOH562 2.9 12.6 1.0 OG1 A:THR64 3.0 21.0 1.0 O A:ASN68 3.1 20.1 1.0 CG A:ASP73 3.4 23.9 1.0 CB A:ASP73 3.4 23.7 1.0 C A:ASN68 4.1 20.5 1.0 N A:SER70 4.2 22.4 1.0 CB A:SER70 4.3 22.9 1.0 O A:ASP73 4.4 23.6 1.0 CB A:THR64 4.5 21.6 1.0 OG A:SER65 4.6 21.3 1.0 OD1 A:ASP73 4.6 25.9 1.0 CA A:LYS69 4.6 21.5 1.0 C A:LYS69 4.7 21.9 1.0 CB A:ASN68 4.7 19.8 1.0 CA A:ASP73 4.8 23.8 1.0 N A:LYS69 4.8 20.9 1.0 N A:SER65 4.8 20.8 1.0 CA A:SER70 4.9 23.0 1.0 N A:THR64 4.9 21.7 1.0

Magnesium binding site 2 out of 3 in the Dimeric SEC14 Family Homolog 3 From Saccharomyces Cerevisiae Presents Some Novel Features of Structure That Lead to A Surprising "Dimer- Monomer" State Change Induced By Substrate Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dimeric SEC14 Family Homolog 3 From Saccharomyces Cerevisiae Presents Some Novel Features of Structure That Lead to A Surprising "Dimer- Monomer" State Change Induced By Substrate Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:13.7 occ:1.00 O B:HOH548 2.6 17.7 1.0 O B:HOH547 2.8 20.1 1.0 O B:HIS232 2.8 13.1 1.0 OH B:TYR93 3.0 14.2 1.0 O B:HOH505 3.1 16.8 1.0 CZ2 B:TRP84 3.5 11.6 1.0 CE2 B:TYR93 3.6 15.1 1.0 CZ B:TYR93 3.6 15.0 1.0 CD B:PRO234 3.6 13.0 1.0 C B:HIS232 3.8 12.4 1.0 O B:HOH502 3.8 14.9 1.0 CH2 B:TRP84 4.1 11.6 1.0 CA B:TYR233 4.1 12.3 1.0 CG2 B:THR111 4.3 12.7 1.0 CG B:PRO234 4.3 13.6 1.0 N B:TYR233 4.4 12.3 1.0 N B:PRO234 4.5 12.9 1.0 CE2 B:TRP84 4.6 12.0 1.0 NH2 B:ARG236 4.7 12.5 1.0 NE B:ARG236 4.7 11.9 1.0 C B:TYR233 4.8 12.6 1.0 CD2 B:TYR93 4.8 15.1 1.0 CA B:HIS232 4.8 12.4 1.0 CD1 B:TYR233 4.9 11.1 1.0 CE1 B:TYR93 4.9 14.5 1.0 NE B:ARG92 5.0 15.0 1.0

Magnesium binding site 3 out of 3 in the Dimeric SEC14 Family Homolog 3 From Saccharomyces Cerevisiae Presents Some Novel Features of Structure That Lead to A Surprising "Dimer- Monomer" State Change Induced By Substrate Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dimeric SEC14 Family Homolog 3 From Saccharomyces Cerevisiae Presents Some Novel Features of Structure That Lead to A Surprising "Dimer- Monomer" State Change Induced By Substrate Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:10.8 occ:1.00 O B:HOH546 2.5 16.8 1.0 NZ B:LYS311 2.6 18.4 1.0 OH B:TYR150 2.7 13.0 1.0 O B:PHE187 2.9 12.8 1.0 O B:LYS26 3.1 24.3 1.0 CZ B:TYR150 3.5 13.7 1.0 CE1 B:TYR150 3.6 13.4 1.0 C B:PHE187 3.6 12.9 1.0 CE B:LYS311 3.7 18.6 1.0 CA B:PHE187 4.1 12.3 1.0 C B:LYS26 4.1 24.3 1.0 O B:MET188 4.2 14.6 1.0 CA B:GLU27 4.2 24.7 1.0 N B:LEU28 4.3 25.2 1.0 C B:MET188 4.3 14.6 1.0 N B:PRO189 4.3 15.2 1.0 CD B:LYS311 4.4 19.6 1.0 CB B:PHE187 4.5 12.2 1.0 CA B:PRO189 4.5 15.8 1.0 CG B:PRO189 4.6 15.8 1.0 C B:GLU27 4.6 25.1 1.0 N B:GLU27 4.6 24.6 1.0 CD1 B:PHE187 4.6 12.5 1.0 N B:MET188 4.7 13.7 1.0 CE2 B:TYR150 4.7 13.4 1.0 CD B:PRO189 4.7 15.3 1.0 CG B:PHE187 4.8 11.7 1.0 CD1 B:TYR150 4.9 12.9 1.0 CB B:PRO189 4.9 15.7 1.0 CD B:GLU27 4.9 25.3 1.0

Y.Yuan, W.Zhao, X.Wang, Y.Gao, L.Niu, M.Teng. Dimeric SFH3 Has Structural Changes in Its Binding Pocket That Are Associated with A Dimer-Monomer State Transformation Induced By Substrate Binding. Acta Crystallogr.,Sect.D V. 69 313 2013.
ISSN: ISSN 0907-4449
PubMed: 23519406
DOI: 10.1107/S0907444912046161